chr7-116700044-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_000245.4(MET):c.960G>A(p.Ala320=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,613,932 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A320A) has been classified as Likely benign.
Frequency
Consequence
NM_000245.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MET | NM_000245.4 | c.960G>A | p.Ala320= | synonymous_variant | 2/21 | ENST00000397752.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MET | ENST00000397752.8 | c.960G>A | p.Ala320= | synonymous_variant | 2/21 | 1 | NM_000245.4 | P3 | |
MET | ENST00000318493.11 | c.960G>A | p.Ala320= | synonymous_variant | 2/21 | 1 | A2 | ||
MET | ENST00000436117.3 | c.960G>A | p.Ala320= | synonymous_variant, NMD_transcript_variant | 2/20 | 1 | |||
MET | ENST00000422097.2 | c.960G>A | p.Ala320= | synonymous_variant | 2/12 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000643 AC: 16AN: 248856Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135008
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461622Hom.: 0 Cov.: 32 AF XY: 0.0000206 AC XY: 15AN XY: 727120
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74478
ClinVar
Submissions by phenotype
Renal cell carcinoma Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 23, 2023 | - - |
Papillary renal cell carcinoma type 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 03, 2015 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at